Bacterial species identification: Difference between revisions
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For 16S rDNA species specific probes, see [http://www.microbial-ecology.de/probebase/ ProbeBase] | For 16S rDNA species specific probes, see [http://www.microbial-ecology.de/probebase/ ProbeBase] | ||
A comprehensive database of 16s and 23s ribosomal sequences can be found here: [http://www.arb-silva.de/ Silva] | |||
| Line 24: | Line 26: | ||
E, Goodfellow M (Wiley, New York), pp 115–175. | E, Goodfellow M (Wiley, New York), pp 115–175. | ||
#Leser02 pmid=11823207 | |||
= | #Alm96 pmid=8837410 | ||
</biblio> | |||
==Universal Bacterial Primers== | ==Universal Bacterial Primers== | ||
| Line 54: | Line 48: | ||
* 1492r 5'TACGGYTACCTTGTTACGACTT | * 1492r 5'TACGGYTACCTTGTTACGACTT | ||
* 1525r 5'AAGGAGGTGWTCCARCC | * 1525r 5'AAGGAGGTGWTCCARCC | ||
==Universal primers from Leser02== | |||
* Edited from Lane91, naming from Alm96, PMID 8837410 | |||
* S-*-Univ-1492-a-A-19 GGTTACCTTGTTACGACTT-3 | |||
* S-D-Bact-0008-a-S-20 AGAGTTTGATCMTGGCTCAG-3 | |||
* S-D-Bact-0907-a-S-20 AAACTCAAAGGAATTGACGG-3 | |||
* S-*-Univ-0519-a-A-18 GTATTACCGCGGCTGCTG-3 | |||
* S-D-Bact-0786-a-A-20 GACTACCAGGGTATCTAATC-3 | |||
* S-D-Bact-1054-a-A-20 ACGAGCTGACGACAGCCATG-3 | |||
==Mycoplasma universal primers== | |||
Johansson K-E, Characterization of mycoplasmas by PCR and sequence analysis with universal 16S rDNA primers, Chapter 18, Mycoplasma Protocols, 1998. | |||
* U1F 12-27 ttg atc ctg gct cag gay daa cg | |||
* U2F 327-348 cca rac tcc tac ggr agg c | |||
* U3R 512-527 att acc gcg gck gct g | |||
* U4F 792-810 gta gtc cac gcc gta aac g | |||
* U5R 902-924 ctt gtg cgg gyy ccc gtc aa | |||
* U6F 1154-1172 gag gaa ggy grg gay gay g | |||
* U7R 1359-1374 aca agr ccc gag aac g | |||
* U8R 1502-1524 gaa agg agg trw tcc ayc csc ac | |||
Latest revision as of 05:49, 25 March 2012
See here for 16S rRNA alignment assistance.
For 16S rDNA species specific probes, see ProbeBase
A comprehensive database of 16s and 23s ribosomal sequences can be found here: Silva
References
- Weisburg WG, Barns SM, Pelletier DA, and Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991 Jan;173(2):697-703. DOI:10.1128/jb.173.2.697-703.1991 |
- Wilson KH, Blitchington RB, and Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol. 1990 Sep;28(9):1942-6. DOI:10.1128/jcm.28.9.1942-1946.1990 |
- Rivas R, Velázquez E, Zurdo-Piñeiro JL, Mateos PF, and Martínez Molina E. Identification of microorganisms by PCR amplification and sequencing of a universal amplified ribosomal region present in both prokaryotes and eukaryotes. J Microbiol Methods. 2004 Mar;56(3):413-26. DOI:10.1016/j.mimet.2003.11.007 |
- Baker GC, Smith JJ, and Cowan DA. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods. 2003 Dec;55(3):541-55. DOI:10.1016/j.mimet.2003.08.009 |
- Watanabe K, Kodama Y, and Harayama S. Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J Microbiol Methods. 2001 Apr;44(3):253-62. DOI:10.1016/s0167-7012(01)00220-2 |
- Böttger EC. Rapid determination of bacterial ribosomal RNA sequences by direct sequencing of enzymatically amplified DNA. FEMS Microbiol Lett. 1989 Nov;53(1-2):171-6. DOI:10.1016/0378-1097(89)90386-8 |
- Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, and Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955-9. DOI:10.1073/pnas.82.20.6955 |
-
Lane DJ (1991) 16S/23S rRNA sequencing. in Nucleic Acid Techniques in Bacterial Systematics, eds Stackebrandt
E, Goodfellow M (Wiley, New York), pp 115–175.
- Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M, and Møller K. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol. 2002 Feb;68(2):673-90. DOI:10.1128/AEM.68.2.673-690.2002 |
- Alm EW, Oerther DB, Larsen N, Stahl DA, and Raskin L. The oligonucleotide probe database. Appl Environ Microbiol. 1996 Oct;62(10):3557-9. DOI:10.1128/aem.62.10.3557-3559.1996 |
Universal Bacterial Primers
Lane, D. J. (1991). 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics. E. Stackebrandt and M. Goodfellow, eds. New York, NY, John Wiley and Sons: 115-175.
- 27f 5'AGAGTTTGATCMTGGCTCAG
- 342r 5'CTGCTGCSYCCCGTAG
- 357f 5'CTCCTACGGGAGGCAGCAG
- 519r 5'GWATTACCGCGGCKGCTG
- 530f 5'GTGCCAGCMGCCGCGG
- 1100r 5'GGGTTGCGCTCGTTG
- 1114f 5'GCAACGAGCGCAACCC
- 1392r 5'ACGGGCGGTGTGTRC
- 1406f 5'TGYACACACCTCCCGT
- 1492r 5'TACGGYTACCTTGTTACGACTT
- 1525r 5'AAGGAGGTGWTCCARCC
Universal primers from Leser02
- Edited from Lane91, naming from Alm96, PMID 8837410
- S-*-Univ-1492-a-A-19 GGTTACCTTGTTACGACTT-3
- S-D-Bact-0008-a-S-20 AGAGTTTGATCMTGGCTCAG-3
- S-D-Bact-0907-a-S-20 AAACTCAAAGGAATTGACGG-3
- S-*-Univ-0519-a-A-18 GTATTACCGCGGCTGCTG-3
- S-D-Bact-0786-a-A-20 GACTACCAGGGTATCTAATC-3
- S-D-Bact-1054-a-A-20 ACGAGCTGACGACAGCCATG-3
Mycoplasma universal primers
Johansson K-E, Characterization of mycoplasmas by PCR and sequence analysis with universal 16S rDNA primers, Chapter 18, Mycoplasma Protocols, 1998.
- U1F 12-27 ttg atc ctg gct cag gay daa cg
- U2F 327-348 cca rac tcc tac ggr agg c
- U3R 512-527 att acc gcg gck gct g
- U4F 792-810 gta gtc cac gcc gta aac g
- U5R 902-924 ctt gtg cgg gyy ccc gtc aa
- U6F 1154-1172 gag gaa ggy grg gay gay g
- U7R 1359-1374 aca agr ccc gag aac g
- U8R 1502-1524 gaa agg agg trw tcc ayc csc ac
